np-workflows 1.6.89__py3-none-any.whl → 1.6.91__py3-none-any.whl

np_workflows/experiments/openscope_loop/camstim_scripts/barcode_opto_script.py

@@ -1,4 +1,3 @@
-# -*- coding: utf-8 -*-
 """
 optotagging.py
 
@@ -9,37 +8,30 @@ by joshs@alleninstitute.org
 (c) 2018 Allen Institute for Brain Science
 
 """
-import camstim  # ensures "magic" gets setup properly by importing first
-import logging  # must occur after camstim import for "magic"
-from camstim.zro import agent
-
-import numpy as np
-from toolbox.IO.nidaq import AnalogOutput
-from toolbox.IO.nidaq import DigitalOutput
 
 import datetime
-import numpy as np
-import time
+import logging  # must occur after camstim import for "magic"
 import pickle as pkl
+import time
 
+import numpy as np
+from camstim.zro import agent
+from toolbox.IO.nidaq import AnalogOutput, DigitalOutput
 
 # %%
 
 
-def run_optotagging(levels, conditions, waveforms, isis, sampleRate=10000.):
-
-    from toolbox.IO.nidaq import AnalogOutput
-    from toolbox.IO.nidaq import DigitalOutput
+def run_optotagging(levels, conditions, waveforms, isis, sampleRate=10000.0):
 
     sweep_on = np.array([0, 0, 1, 0, 0, 0, 0, 0], dtype=np.uint8)
     stim_on = np.array([0, 0, 1, 1, 0, 0, 0, 0], dtype=np.uint8)
     stim_off = np.array([0, 0, 1, 0, 0, 0, 0, 0], dtype=np.uint8)
     sweep_off = np.array([0, 0, 0, 0, 0, 0, 0, 0], dtype=np.uint8)
 
-    ao = AnalogOutput('Dev1', channels=[1])
+    ao = AnalogOutput("Dev1", channels=[1])
     ao.cfg_sample_clock(sampleRate)
 
-    do = DigitalOutput('Dev1', 2)
+    do = DigitalOutput("Dev1", 2)
 
     do.start()
     ao.start()
@@ -62,71 +54,123 @@ def run_optotagging(levels, conditions, waveforms, isis, sampleRate=10000.):
     do.clear()
     ao.clear()
 
+
 # %%
 
 
-def generatePulseTrain(pulseWidth, pulseInterval, numRepeats, riseTime, sampleRate=10000.):
+def generatePulseTrain(
+    pulseWidth, pulseInterval, numRepeats, riseTime, sampleRate=10000.0
+):
 
     data = np.zeros((int(sampleRate),), dtype=np.float64)
-   # rise_samples =
+    # rise_samples =
 
     rise_and_fall = (
-        ((1 - np.cos(np.arange(sampleRate*riseTime/1000., dtype=np.float64)*2*np.pi/10))+1)-1)/2
+        (
+            (
+                1
+                - np.cos(
+                    np.arange(sampleRate * riseTime / 1000.0, dtype=np.float64)
+                    * 2
+                    * np.pi
+                    / 10
+                )
+            )
+            + 1
+        )
+        - 1
+    ) / 2
     half_length = rise_and_fall.size / 2
     rise = rise_and_fall[:half_length]
     fall = rise_and_fall[half_length:]
 
-    peak_samples = int(sampleRate*(pulseWidth-riseTime*2)/1000)
+    peak_samples = int(sampleRate * (pulseWidth - riseTime * 2) / 1000)
     peak = np.ones((peak_samples,))
 
-    pulse = np.concatenate((rise,
-                            peak,
-                            fall))
+    pulse = np.concatenate((rise, peak, fall))
 
-    interval = int(pulseInterval*sampleRate/1000.)
+    interval = int(pulseInterval * sampleRate / 1000.0)
 
     for i in range(0, numRepeats):
-        data[i*interval:i*interval+pulse.size] = pulse
+        data[i * interval : i * interval + pulse.size] = pulse
 
     return data
 
 
 # %% create waveforms
 
-def optotagging(mouseID, operation_mode='experiment', level_list=[1.15, 1.28, 1.345], genotype=None):
+
+def optotagging(
+    mouseID, operation_mode="experiment", level_list=[1.15, 1.28, 1.345], genotype=None
+):
 
     sampleRate = 10000
 
     # 1 s cosine ramp:
-    data_cosine = (((1 - np.cos(np.arange(sampleRate, dtype=np.float64)
-                                * 2*np.pi/sampleRate)) + 1) - 1)/2  # create raised cosine waveform
+    data_cosine = (
+        (
+            (
+                1
+                - np.cos(
+                    np.arange(sampleRate, dtype=np.float64) * 2 * np.pi / sampleRate
+                )
+            )
+            + 1
+        )
+        - 1
+    ) / 2  # create raised cosine waveform
 
     # 1 ms cosine ramp:
     rise_and_fall = (
-        ((1 - np.cos(np.arange(sampleRate*0.001, dtype=np.float64)*2*np.pi/10))+1)-1)/2
+        (
+            (
+                1
+                - np.cos(
+                    np.arange(sampleRate * 0.001, dtype=np.float64) * 2 * np.pi / 10
+                )
+            )
+            + 1
+        )
+        - 1
+    ) / 2
     half_length = rise_and_fall.size / 2
 
     # pulses with cosine ramp:
-    pulse_2ms = np.concatenate((rise_and_fall[:half_length], np.ones(
-        (int(sampleRate*0.001),)), rise_and_fall[half_length:]))
-    pulse_5ms = np.concatenate((rise_and_fall[:half_length], np.ones(
-        (int(sampleRate*0.004),)), rise_and_fall[half_length:]))
-    pulse_10ms = np.concatenate((rise_and_fall[:half_length], np.ones(
-        (int(sampleRate*0.009),)), rise_and_fall[half_length:]))
+    pulse_2ms = np.concatenate(
+        (
+            rise_and_fall[:half_length],
+            np.ones((int(sampleRate * 0.001),)),
+            rise_and_fall[half_length:],
+        )
+    )
+    pulse_5ms = np.concatenate(
+        (
+            rise_and_fall[:half_length],
+            np.ones((int(sampleRate * 0.004),)),
+            rise_and_fall[half_length:],
+        )
+    )
+    pulse_10ms = np.concatenate(
+        (
+            rise_and_fall[:half_length],
+            np.ones((int(sampleRate * 0.009),)),
+            rise_and_fall[half_length:],
+        )
+    )
 
     data_2ms_10Hz = np.zeros((sampleRate,), dtype=np.float64)
 
     for i in range(0, 10):
         interval = sampleRate / 10
-        data_2ms_10Hz[i*interval:i*interval+pulse_2ms.size] = pulse_2ms
+        data_2ms_10Hz[i * interval : i * interval + pulse_2ms.size] = pulse_2ms
 
     data_5ms = np.zeros((sampleRate,), dtype=np.float64)
-    data_5ms[:pulse_5ms.size] = pulse_5ms
+    data_5ms[: pulse_5ms.size] = pulse_5ms
 
     data_10ms = np.zeros((sampleRate,), dtype=np.float64)
-    data_10ms[:pulse_10ms.size] = pulse_10ms
+    data_10ms[: pulse_10ms.size] = pulse_10ms
 
-    data_10s = np.zeros((sampleRate*10,), dtype=np.float64)
+    data_10s = np.zeros((sampleRate * 10,), dtype=np.float64)
     data_10s[:-2] = 1
 
     # %% for experiment
@@ -138,8 +182,8 @@ def optotagging(mouseID, operation_mode='experiment', level_list=[1.15, 1.28, 1.
     condition_list = [2, 3]
     waveforms = [data_2ms_10Hz, data_5ms, data_10ms, data_cosine]
 
-    opto_levels = np.array(level_list*numRepeats*len(condition_list))  # BLUE
-    opto_conditions = condition_list*numRepeats*len(level_list)
+    opto_levels = np.array(level_list * numRepeats * len(condition_list))  # BLUE
+    opto_conditions = condition_list * numRepeats * len(level_list)
     opto_conditions = np.sort(opto_conditions)
     opto_isis = np.random.random(opto_levels.shape) * isi_rand + isi
 
@@ -151,7 +195,7 @@ def optotagging(mouseID, operation_mode='experiment', level_list=[1.15, 1.28, 1.
 
     # %% for testing
 
-    if operation_mode == 'test_levels':
+    if operation_mode == "test_levels":
         isi = 2.0
         isi_rand = 0.0
 
@@ -160,60 +204,69 @@ def optotagging(mouseID, operation_mode='experiment', level_list=[1.15, 1.28, 1.
         condition_list = [0]
         waveforms = [data_10s, data_10s]
 
-        opto_levels = np.array(level_list*numRepeats *
-                               len(condition_list))  # BLUE
-        opto_conditions = condition_list*numRepeats*len(level_list)
+        opto_levels = np.array(level_list * numRepeats * len(condition_list))  # BLUE
+        opto_conditions = condition_list * numRepeats * len(level_list)
         opto_conditions = np.sort(opto_conditions)
         opto_isis = np.random.random(opto_levels.shape) * isi_rand + isi
 
-    elif operation_mode == 'pretest':
+    elif operation_mode == "pretest":
         numRepeats = 1
 
         condition_list = [0]
-        data_2s = data_10s[-sampleRate*2:]
+        data_2s = data_10s[-sampleRate * 2 :]
         waveforms = [data_2s]
 
-        opto_levels = np.array(level_list*numRepeats *
-                               len(condition_list))  # BLUE
-        opto_conditions = condition_list*numRepeats*len(level_list)
+        opto_levels = np.array(level_list * numRepeats * len(condition_list))  # BLUE
+        opto_conditions = condition_list * numRepeats * len(level_list)
         opto_conditions = np.sort(opto_conditions)
-        opto_isis = [1]*len(opto_conditions)
+        opto_isis = [1] * len(opto_conditions)
     # %%
 
     outputDirectory = agent.OUTPUT_DIR
-    fileDate = str(datetime.datetime.now()).replace(':', '').replace(
-        '.', '').replace('-', '').replace(' ', '')[2:14]
-    fileName = outputDirectory  + "/" + fileDate + '_'+mouseID + '.opto.pkl'
-
-    print('saving info to: ' + fileName)
-    fl = open(fileName, 'wb')
+    fileDate = (
+        str(datetime.datetime.now())
+        .replace(":", "")
+        .replace(".", "")
+        .replace("-", "")
+        .replace(" ", "")[2:14]
+    )
+    fileName = outputDirectory + "/" + fileDate + "_" + mouseID + ".opto.pkl"
+
+    print("saving info to: " + fileName)
+    fl = open(fileName, "wb")
     output = {}
 
-    output['opto_levels'] = opto_levels
-    output['opto_conditions'] = opto_conditions
-    output['opto_ISIs'] = opto_isis
-    output['opto_waveforms'] = waveforms
+    output["opto_levels"] = opto_levels
+    output["opto_conditions"] = opto_conditions
+    output["opto_ISIs"] = opto_isis
+    output["opto_waveforms"] = waveforms
 
     pkl.dump(output, fl)
     fl.close()
-    print('saved.')
+    print("saved.")
 
     # %%
-    run_optotagging(opto_levels, opto_conditions,
-                    waveforms, opto_isis, float(sampleRate))
+    run_optotagging(
+        opto_levels, opto_conditions, waveforms, opto_isis, float(sampleRate)
+    )
 
 
 # %%
 if __name__ == "__main__":
-    import json
     import argparse
+    import json
 
     parser = argparse.ArgumentParser()
-    parser.add_argument('json_params', type=str, )
+    parser.add_argument(
+        "json_params",
+        type=str,
+    )
     args, _ = parser.parse_known_args()
 
-    with open(args.json_params, 'r', ) as f:
+    with open(
+        args.json_params,
+    ) as f:
         json_params = json.load(f)
 
-    logging.info('Optotagging with params: %s' % json_params)
+    logging.info("Optotagging with params: %s" % json_params)
     optotagging(**json_params)

np_workflows/experiments/openscope_loop/loop_workflow_widget.py

@@ -1,17 +1,6 @@
-import configparser
-import contextlib
-import copy
-import enum
-import functools
-from typing import ClassVar, Literal, NamedTuple, NoReturn, Optional, TypedDict
-
 import IPython.display
 import ipywidgets as ipw
-import np_config
-import np_logging
 import np_session
-import np_workflows
-from pyparsing import Any
 
 from np_workflows.experiments.openscope_loop.main_loop_pilot import LoopSession
 
@@ -20,6 +9,7 @@ global_state = {}
 
 # for widget, before creating a experiment --------------------------------------------- #
 
+
 class SelectedSession:
     def __init__(self, session: str | LoopSession, mouse: str | int | np_session.Mouse):
         if isinstance(session, str):
@@ -48,17 +38,19 @@ def loop_workflow_widget(
         options=tuple(_.value for _ in LoopSession),
         description="Session",
     )
-    
+
     def update_selection():
         selection.__init__(str(session_dropdown.value), str(mouse))
-        
-    if (previously_selected_value := global_state.get('selected_session')):
+
+    if previously_selected_value := global_state.get("selected_session"):
         session_dropdown.value = previously_selected_value
         update_selection()
-        
+
     console = ipw.Output()
     with console:
-        if last_session := np_session.Mouse(selection.mouse).state.get('last_loop_session'):
+        if last_session := np_session.Mouse(selection.mouse).state.get(
+            "last_loop_session"
+        ):
             print(f"{mouse} last session: {last_session}")
         print(f"Selected: {selection.session}")
 
@@ -74,9 +66,9 @@ def loop_workflow_widget(
         update_selection()
         with console:
             print(f"Selected: {selection.session}")
-        global_state['selected_session'] = selection.session.value
-        
-    session_dropdown.observe(update, names='value')
+        global_state["selected_session"] = selection.session.value
+
+    session_dropdown.observe(update, names="value")
 
     IPython.display.display(ipw.VBox([session_dropdown, console]))
 

np_workflows/experiments/openscope_loop/main_loop_pilot.py

@@ -1,41 +1,22 @@
-import configparser
 import contextlib
-import copy
-import dataclasses
-import datetime
 import enum
-import functools
-import pathlib
-import platform
-import shutil
-import threading
 import time
-import zlib
-from typing import ClassVar, Literal, NamedTuple, NoReturn, Optional, TypedDict
 
-import IPython
-import IPython.display
-import ipywidgets as ipw
-import np_config
 import np_logging
-import np_services
 import np_session
-import np_workflows
-import PIL.Image
-import pydantic
-from pyparsing import Any
 from np_services import (
-    Service,
     Finalizable,
-    ScriptCamstim, SessionCamstim, 
-    SessionCamstim,
+    MouseDirector,
+    NewScaleCoordinateRecorder,
     OpenEphys,
+    Service,
+    SessionCamstim,
     Sync,
     VideoMVR,
-    NewScaleCoordinateRecorder,
-    MouseDirector,
 )
 
+import np_workflows
+
 logger = np_logging.getLogger(__name__)
 
 
@@ -49,16 +30,16 @@ class LoopSession(enum.Enum):
 
 class LoopMixin:
     """Provides project-specific methods and attributes, mainly related to camstim scripts."""
-    
+
     workflow: LoopSession
     """Enum for particular workflow/session, e.g. PRETEST, HAB_60, HAB_90,
     EPHYS."""
-    
+
     session: np_session.PipelineSession
     mouse: np_session.Mouse
     user: np_session.User
     platform_json: np_session.PlatformJson
-    
+
     @property
     def recorders(self) -> tuple[Service, ...]:
         """Services to be started before stimuli run, and stopped after. Session-dependent."""
@@ -70,11 +51,11 @@ class LoopMixin:
 
     @property
     def stims(self) -> tuple[Service, ...]:
-        return (SessionCamstim, )
-    
+        return (SessionCamstim,)
+
     def initialize_and_test_services(self) -> None:
         """Configure, initialize (ie. reset), then test all services."""
-        
+
         MouseDirector.user = self.user.id
         MouseDirector.mouse = self.mouse.id
 
@@ -92,79 +73,95 @@ class LoopMixin:
 
     def update_state(self) -> None:
         "Store useful but non-essential info."
-        self.mouse.state['last_session'] = self.session.id
-        self.mouse.state['last_Loop_session'] = str(self.workflow)
+        self.mouse.state["last_session"] = self.session.id
+        self.mouse.state["last_Loop_session"] = str(self.workflow)
         if self.mouse == 366122:
             return
         match self.workflow:
             case LoopSession.PRETEST:
                 return
             case LoopSession.HAB:
-                self.session.project.state['latest_hab'] = self.session.id
+                self.session.project.state["latest_hab"] = self.session.id
             case LoopSession.EPHYS:
-                self.session.project.state['latest_ephys'] = self.session.id
-                self.session.project.state['sessions'] = self.session.project.state.get('sessions', []) + [self.session.id]
-                
+                self.session.project.state["latest_ephys"] = self.session.id
+                self.session.project.state["sessions"] = self.session.project.state.get(
+                    "sessions", []
+                ) + [self.session.id]
+
     def run_stim(self) -> None:
 
         self.update_state()
-        
+
         if not SessionCamstim.is_ready_to_start():
             raise RuntimeError("SessionCamstim is not ready to start.")
-        
-        np_logging.web(f'Loop_{self.workflow.name.lower()}').info(f"Started session {self.mouse.mtrain.stage['name']}")
+
+        np_logging.web(f"Loop_{self.workflow.name.lower()}").info(
+            f"Started session {self.mouse.mtrain.stage['name']}"
+        )
         SessionCamstim.start()
-        
+
         with contextlib.suppress(Exception):
             while not SessionCamstim.is_ready_to_start():
                 time.sleep(2.5)
-            
+
         if isinstance(SessionCamstim, Finalizable):
             SessionCamstim.finalize()
 
         with contextlib.suppress(Exception):
-            np_logging.web(f'Loop_{self.workflow.name.lower()}').info(f"Finished session {self.mouse.mtrain.stage['name']}")
-    
-    
-    def copy_data_files(self) -> None: 
+            np_logging.web(f"Loop_{self.workflow.name.lower()}").info(
+                f"Finished session {self.mouse.mtrain.stage['name']}"
+            )
+
+    def copy_data_files(self) -> None:
         super().copy_data_files()
-        
+
         # When all processing completes, camstim Agent class passes data and uuid to
         # /camstim/lims BehaviorSession class, and write_behavior_data() writes a
         # final .pkl with default name YYYYMMDDSSSS_mouseID_foragingID.pkl
         # - if we have a foraging ID, we can search for that
-        if None == (stim_pkl := next(self.session.npexp_path.glob(f'{self.session.date:%y%m%d}*_{self.session.mouse}_*.pkl'), None)):
-            logger.warning('Did not find stim file on npexp matching the format `YYYYMMDDSSSS_mouseID_foragingID.pkl`')
+        if None == (
+            stim_pkl := next(
+                self.session.npexp_path.glob(
+                    f"{self.session.date:%y%m%d}*_{self.session.mouse}_*.pkl"
+                ),
+                None,
+            )
+        ):
+            logger.warning(
+                "Did not find stim file on npexp matching the format `YYYYMMDDSSSS_mouseID_foragingID.pkl`"
+            )
             return
         assert stim_pkl
         if not self.session.platform_json.foraging_id:
-            self.session.platform_json.foraging_id = stim_pkl.stem.split('_')[-1]
-        new_stem = f'{self.session.folder}.stim'
-        logger.debug(f'Renaming stim file copied to npexp: {stim_pkl} -> {new_stem}')
+            self.session.platform_json.foraging_id = stim_pkl.stem.split("_")[-1]
+        new_stem = f"{self.session.folder}.stim"
+        logger.debug(f"Renaming stim file copied to npexp: {stim_pkl} -> {new_stem}")
         stim_pkl = stim_pkl.rename(stim_pkl.with_stem(new_stem))
-        
+
         # remove other stim pkl, which is nearly identical, if it was also copied
-        for pkl in self.session.npexp_path.glob('*.pkl'):
+        for pkl in self.session.npexp_path.glob("*.pkl"):
             if (
                 self.session.folder not in pkl.stem
-                and 
-                abs(pkl.stat().st_size - stim_pkl.stat().st_size) < 1e6
+                and abs(pkl.stat().st_size - stim_pkl.stat().st_size) < 1e6
             ):
-                logger.debug(f'Deleting extra stim pkl copied to npexp: {pkl.stem}')
+                logger.debug(f"Deleting extra stim pkl copied to npexp: {pkl.stem}")
                 pkl.unlink()
-        
-        
+
+
 def validate_selected_workflow(session: LoopSession, mouse: np_session.Mouse) -> None:
-    for workflow in ('hab', 'ephys'):
+    for workflow in ("hab", "ephys"):
         if (
             workflow in session.value.lower()
-            and workflow not in mouse.mtrain.stage['name'].lower()
+            and workflow not in mouse.mtrain.stage["name"].lower()
         ) or (
-            session.value.lower() == 'ephys' and 'hab' in mouse.mtrain.stage['name'].lower()
+            session.value.lower() == "ephys"
+            and "hab" in mouse.mtrain.stage["name"].lower()
         ):
-            raise ValueError(f"Workflow selected ({session.value}) does not match MTrain stage ({mouse.mtrain.stage['name']}): please check cells above.")
+            raise ValueError(
+                f"Workflow selected ({session.value}) does not match MTrain stage ({mouse.mtrain.stage['name']}): please check cells above."
+            )
+
 
-    
 class Hab(LoopMixin, np_workflows.PipelineHab):
     def __init__(self, *args, **kwargs):
         self.services = (
@@ -209,9 +206,10 @@ def new_experiment(
         case _:
             raise ValueError(f"Invalid workflow type: {workflow}")
     experiment.workflow = workflow
-    
+
     with contextlib.suppress(Exception):
-        np_logging.web(f'Loop_{experiment.workflow.name.lower()}').info(f"{experiment} created")
-            
-    return experiment
+        np_logging.web(f"Loop_{experiment.workflow.name.lower()}").info(
+            f"{experiment} created"
+        )
 
+    return experiment

np_workflows/experiments/openscope_psycode/__init__.py

@@ -1,2 +1,2 @@
-from .main_psycode_pilot import new_experiment, Hab, Ephys, validate_selected_workflow
+from .main_psycode_pilot import Ephys, Hab, new_experiment, validate_selected_workflow
 from .psycode_workflow_widget import PsyCode_workflow_widget